Watershed Maps

1. AOI’s & projection

crs_master <- st_crs("epsg:4326")
aoi_site   = sf::read_sf("./assets/inputs/chilwa_watershed_4326.shp") |>
  st_cast() |> st_transform(crs_master)
aoi_country <- giscoR::gisco_get_countries(country = "Malawi", resolution = "3") |>
  st_cast() |>
  st_transform(crs_master)

# Interactive map mode: "view"
tmap::tmap_mode("view")
tmap::tm_shape(aoi_country) +
  tmap::tm_borders(lwd = 1, col = "green") +
  tmap::tm_shape(aoi_site) +
  tmap::tm_borders(lwd = 2, col = "red")

Figure 1: Interactive map showing area of interest polygons (AOI)

2. Download hydro data

url_rivers <- "https://data.hydrosheds.org/file/HydroRIVERS/HydroRIVERS_v10_shp.zip"
url_lakes <- "https://data.hydrosheds.org/file/hydrolakes/HydroLAKES_polys_v10_shp.zip"
url_watersheds <- "https://data.hydrosheds.org/file/hydrobasins/customized_with_lakes/hybas_lake_af_lev01-12_v1c.zip"
# download.file(url = url, path = getwd(), destfile = file_name)

rivers = sf::st_read("~/Repos/datasets/hydrography/HydroRIVERS_v10_shp/HydroRIVERS_v10.shp") |> 
  sf::st_cast() |> sf::st_transform(crs_master)
lakes = sf::st_read("~/Repos/datasets/hydrography/HydroLAKES_polys_v10_shp/HydroLAKES_polys_v10.shp") |> 
  sf::st_cast() |> sf::st_transform(crs_master)
watershed = sf::st_read("~/Repos/datasets/hydrography/hybas_lake_af_lev01-12_v1c/hybas_lake_af_lev04_v1c.shp") |> 
  sf::st_cast() |> sf::st_transform(crs_master)

rivers_country     = sf::st_intersection(rivers, aoi_country)
rivers_site        = sf::st_intersection(rivers, aoi_site)
lakes_country      = sf::st_intersection(lakes, aoi_country)
lakes_site         = sf::st_intersection(lakes, aoi_site)
watershed_country = sf::st_intersection(watershed, aoi_country)
watershed_site    = sf::st_intersection(watershed, aoi_site)
# reproject if NAs outputed, caution of long processing time
# watersheds <- terra::project(watersheds, crs(aoi_site))

# save extracted layers for faster runtime
sf::st_write(rivers_country, "./assets/inputs/rivers_country.shp")
sf::st_write(rivers_site, "./assets/inputs/rivers_site.shp")
sf::st_write(lakes_country, "./assets/inputs/lakes_country.shp")
sf::st_write(lakes_site, "./assets/inputs/lakes_site.shp")
sf::st_write(watershed_country, "./assets/inputs/watershed_country.shp")
sf::st_write(watershed_site, "./assets/inputs/watershed_site.shp")

tmap::tm_shape(rivers_site) + tm_lines(col = "steelblue") +
  tmap::tm_shape(lakes_site) + tm_fill ("steelblue") +
  tmap::tm_shape(watershed_site) + tm_borders(col = "red", lwd=1)

Figure 2: Interactive map showing extracted hydrographic layers

3. Download DEM

dem_site = elevatr::get_elev_raster(
  locations = watershed_site,
  z = 10, clip = "locations")

dem_site = dem_site |>
  terra::rast() |>
  terra::project(crs(watershed_site))

names(dem_site)[1] <- "Elevation (m asl)"

tmap::tm_shape(dem_site) +
    tm_raster(col.scale = tm_scale_continuous(values = terrain.colors(9))) +
  tmap::tm_shape(rivers_site) + tm_lines(col = "steelblue") +
  tmap::tm_shape(lakes_site) + tm_fill ("steelblue") +
  tmap::tm_shape(watershed_site) + tm_borders(col = "red", lwd=1)

Figure 3: Interactive map showing digital elevation model and hydrographic layers

4. Build 3D map

rivers_strahler = rivers_site |>
  dplyr::mutate(
    width = as.numeric(
      ORD_FLOW
    ),
    width = dplyr::case_when(
      width == 3 ~ 16,
      width == 4 ~ 14,
      width == 5 ~ 12,
      width == 6 ~ 10,
      width == 7 ~ 6,
      TRUE ~ 0
    )
  ) |>
  sf::st_as_sf() |>
  sf::st_transform(crs = "epsg:4326")

h <- nrow(dem_site)
w <- ncol(dem_site)

dem_matrix = rayshader::raster_to_matrix(dem_site)

dem_matrix |>
  rayshader:: height_shade() |>
  rayshader::add_overlay(
    rayshader::generate_line_overlay(
      geometry   = rivers_strahler,
      extent     = dem_site,
      heightmap  = dem_matrix,
      color      = "#387B9C",
      linewidth  = rivers_strahler$width,
      data_column_width = "width"
      ), alphalayer = 1
    ) |>
  rayshader::add_overlay(
    rayshader::generate_line_overlay(
      geometry   = lakes_site,
      extent     = dem_site,
      heightmap  = dem_matrix,
      color      = "#387B9C"
      ), alphalayer = 1
    ) |>
  rayshader::plot_3d(
    dem_matrix,
    zscale       = 14,
    solid        = T,
    shadow       = T,
    shadow_darkness = 2,
    background   = "white",
    windowsize   = c(600, 600),
    zoom         = 0.6,
    phi          = 40,
    theta        = 0 
  )

5. Render 3D map

rayshader::render_highquality(
  preview        = T,
  light          = F,
  lightdirection = c(135, 45),
  lightcolor = c("white"),
  lightaltitude = 25,
  ambient_light = 0.1,
  rotate_env     = 0.4,
  intensity_env  = 0.85,
  interactive    = F,
  parallel       = T,
  width          = w,
  height         = h,
  backgroundhigh="#FFFFFF",
  backgroundlow="#FFFFFF"
  )

Figure 4: Three-dimensional map of Lake Chilwa watershed
devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.2 Patched (2024-11-18 r87347)
 os       macOS Sequoia 15.1.1
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Vancouver
 date     2024-11-27
 pandoc   3.5 @ /usr/local/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
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 rlang                1.1.4      2024-06-04 [1] CRAN (R 4.4.0)
 rmarkdown            2.29       2024-11-04 [1] CRAN (R 4.4.1)
 rpart                4.1.23     2023-12-05 [1] CRAN (R 4.4.2)
 rsconnect          * 1.3.3      2024-11-19 [1] CRAN (R 4.4.1)
 RSpectra             0.16-2     2024-07-18 [1] CRAN (R 4.4.0)
 rstatix              0.7.2      2023-02-01 [1] CRAN (R 4.4.0)
 RStoolbox          * 1.0.0      2024-04-25 [1] CRAN (R 4.4.0)
 rstudioapi           0.17.1     2024-10-22 [1] CRAN (R 4.4.1)
 rts                * 1.1-14     2023-10-01 [1] CRAN (R 4.4.0)
 Rttf2pt1             1.3.12     2023-01-22 [1] CRAN (R 4.4.0)
 Ryacas0              0.4.4      2023-01-12 [1] CRAN (R 4.4.0)
 s2                 * 1.1.7      2024-07-17 [1] CRAN (R 4.4.0)
 sandwich             3.1-1      2024-09-15 [1] CRAN (R 4.4.1)
 sass                 0.4.9      2024-03-15 [1] CRAN (R 4.4.0)
 satellite            1.0.5      2024-02-10 [1] CRAN (R 4.4.0)
 scales             * 1.3.0      2023-11-28 [1] CRAN (R 4.4.0)
 sessioninfo          1.2.2      2021-12-06 [1] CRAN (R 4.4.0)
 settings             0.2.7      2021-05-07 [1] CRAN (R 4.4.0)
 sf                 * 1.0-19     2024-11-05 [1] CRAN (R 4.4.1)
 shiny                1.9.1      2024-08-01 [1] CRAN (R 4.4.0)
 shinyjs              2.1.0      2021-12-23 [1] CRAN (R 4.4.0)
 sits               * 1.5.1      2024-08-19 [1] CRAN (R 4.4.1)
 slippymath           0.3.1      2019-06-28 [1] CRAN (R 4.4.0)
 sp                 * 2.1-4      2024-04-30 [1] CRAN (R 4.4.0)
 spacesXYZ            1.3-0      2024-01-23 [1] CRAN (R 4.4.0)
 spData             * 2.3.3      2024-09-02 [1] CRAN (R 4.4.1)
 spdep              * 1.3-6      2024-09-13 [1] CRAN (R 4.4.1)
 stars              * 0.6-7      2024-11-07 [1] CRAN (R 4.4.1)
 StempCens            1.1.0      2020-10-21 [1] CRAN (R 4.4.0)
 stringi              1.8.4      2024-05-06 [1] CRAN (R 4.4.0)
 stringr            * 1.5.1      2023-11-14 [1] CRAN (R 4.4.0)
 supercells         * 1.0.0      2024-02-11 [1] CRAN (R 4.4.0)
 survival             3.7-0      2024-06-05 [1] CRAN (R 4.4.2)
 tensorA              0.36.2.1   2023-12-13 [1] CRAN (R 4.4.0)
 terra              * 1.7-78     2024-05-22 [1] CRAN (R 4.4.0)
 terrainr           * 0.7.5      2023-10-04 [1] CRAN (R 4.4.0)
 testthat           * 3.2.1.1    2024-04-14 [1] CRAN (R 4.4.0)
 tibble             * 3.2.1      2023-03-20 [1] CRAN (R 4.4.0)
 tidyr              * 1.3.1      2024-01-24 [1] CRAN (R 4.4.0)
 tidyselect           1.2.1      2024-03-11 [1] CRAN (R 4.4.0)
 tidyterra          * 0.6.1      2024-06-08 [1] CRAN (R 4.4.0)
 tidyverse          * 2.0.0      2023-02-22 [1] CRAN (R 4.4.0)
 timechange           0.3.0      2024-01-18 [1] CRAN (R 4.4.0)
 timeDate             4041.110   2024-09-22 [1] CRAN (R 4.4.1)
 tlrmvnmvt            1.1.2      2022-06-09 [1] CRAN (R 4.4.0)
 tmap               * 3.99.9003  2024-11-22 [1] Github (r-tmap/tmap@72c1edf)
 tmaptools          * 3.1-1      2021-01-19 [1] CRAN (R 4.4.0)
 tmvtnorm             1.6        2023-12-05 [1] CRAN (R 4.4.0)
 torch                0.13.0     2024-05-21 [1] CRAN (R 4.4.0)
 tzdb                 0.4.0      2023-05-12 [1] CRAN (R 4.4.0)
 unifir               0.2.4      2024-02-01 [1] CRAN (R 4.4.0)
 units                0.8-5      2023-11-28 [1] CRAN (R 4.4.0)
 urlchecker           1.0.1      2021-11-30 [1] CRAN (R 4.4.0)
 usethis              3.0.0      2024-07-29 [1] CRAN (R 4.4.0)
 utf8                 1.2.4      2023-10-22 [1] CRAN (R 4.4.0)
 vctrs                0.6.5      2023-12-01 [1] CRAN (R 4.4.0)
 viridis              0.6.5      2024-01-29 [1] CRAN (R 4.4.0)
 viridisLite          0.4.2      2023-05-02 [1] CRAN (R 4.4.0)
 visNetwork           2.1.2      2022-09-29 [1] CRAN (R 4.4.0)
 withr                3.0.2      2024-10-28 [1] CRAN (R 4.4.1)
 wk                   0.9.4      2024-10-11 [1] CRAN (R 4.4.1)
 xfun                 0.49       2024-10-31 [1] CRAN (R 4.4.1)
 xgboost            * 1.7.8.1    2024-07-24 [1] CRAN (R 4.4.0)
 XML                  3.99-0.17  2024-06-25 [1] CRAN (R 4.4.0)
 xml2                 1.3.6      2023-12-04 [1] CRAN (R 4.4.0)
 xtable               1.8-4      2019-04-21 [1] CRAN (R 4.4.0)
 xts                * 0.14.1     2024-10-15 [1] CRAN (R 4.4.1)
 yaml                 2.3.10     2024-07-26 [1] CRAN (R 4.4.0)
 yulab.utils          0.1.8      2024-11-07 [1] CRAN (R 4.4.1)
 zeallot              0.1.0      2018-01-28 [1] CRAN (R 4.4.0)
 zip                  2.3.1      2024-01-27 [1] CRAN (R 4.4.0)
 zoo                * 1.8-12     2023-04-13 [1] CRAN (R 4.4.0)

 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library

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